bioRxiv preprint doi: https://doi.org/10.1101/2021.06.15.448470; this version posted June 15, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Systematic Chromosome Rearrangement Induced by CRISPR-Cas9 Reshapes the Genome and Transcriptome of Human Cells Ying Liu1#, Guangwei Ma1,2#, Zenghong Gao1, Jian Li1, Jin Wang1, Xiangping Zhu1, Jiawen Yang1,3, Yiting Zhou1, Kaishun, Hu1, Yin Zhang1*, Yabin Guo1* Affiliation: 1Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120; 2Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158; 3State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China. #equal contributions *Correspondence: [email protected]; [email protected] Running title: Genome shuffle by CRISPR-Cas9 Highlights: Repetitive retroelements with large copy numbers were targeted using CRISPR-Cas9 in human cells. Cells survived after their chromosomal DNAs were heavily cleaved and systematic chromosome rearrangement was achieved. Systematic chromosome rearrangement reshaped the genome and transcriptome of the cells. bioRxiv preprint doi: https://doi.org/10.1101/2021.06.15.448470; this version posted June 15, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Chromosome rearrangement plays important roles in development, carcinogenesis and evolution. However, its mechanism and subsequent effects are not fully understood. At present, large-scale chromosome rearrangement has been performed in the simple eukaryote, wine yeast, but the relative research in mammalian cells remains at the level of individual chromosome rearrangement due to technical limitations. In this study, we used CRISPR-Cas9 to target the highly repetitive human endogenous retrotransposons, LINE-1 (L1) and Alu, resulting in a large number of DNA double-strand breaks in the chromosomes. While this operation killed the majority of the cells, we eventually obtained live cell groups. Karyotype analysis and genome re-sequencing proved that we have achieved systematic chromosome rearrangement (SCR) in human cells. The copy number variations (CNVs) of the SCR genomes showed typical patterns that observed in tumor genomes. For example, the most frequent deleted region Chr9p21 containing p15 and p16 tumor suppressor, and the amplified region Chr8q24 containing MYC in tumors were all identified in both SCR cells. The ATAC-seq and RNA-seq further revealed that the epigenetic and transcriptomic landscapes were deeply reshaped by the SCR. Gene expressions related to p53 pathway, DNA repair, cell cycle and apoptosis were greatly altered to facilitate the cell survival under the severe stress induced by the large-scale chromosomal breaks. In addition, we found that the cells acquired CRISPR-Cas9 resistance after SCR by interfering with the Cas9 mRNA. Our study provided a new application of CRISPR-Cas9 and a practical approach for SCR in complex mammalian genomes. Keywords: CRISPR-Cas9, chromosome rearrangement, human genome, retrotransposon, LINE-1, Alu. bioRxiv preprint doi: https://doi.org/10.1101/2021.06.15.448470; this version posted June 15, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Introduction Chromosome rearrangements are mutations that cause genomic structural variations, including insertions, deletions, duplications, copy-number variations (CNVs), inversions and translocations. Chromosome rearrangements are usually caused by DNA double strand breaks (DSBs) and rejoins1. It is known that 0.5% of neonatal genomes have abnormalities caused by chromosome rearrangements2. The famous Robertsonian translocations occur between the human acrocentric chromosomes (chr13, 14, 15, 21, 22 and Y), which may have normal phenotype, but sometime can cause Downs syndrome or other diseases3. Chromosome rearrangements also contribute for carcinogenesis4. For example, the Philadelphia chromosome is a rearrangement between chromosome 9 and 22, which makes ABL1 and the strong promoter of BCR (break point cluster region) fuse to form BCR-ABL chimeric gene, resulting in continuous high expression of ABL1 kinase and cell transformation5. Moreover, Chromosome rearrangement is a major motivation for evolution6. Chromosome rearrangements not only change the primary structure of DNA, but also change the three-dimensional (3D) conformation of chromatins7. One of the most extreme examples so far is that Shao et al. Combined 16 chromosomes of Saccharomyces cerevisiae into one, creating a yeast strain with only one chromosome in 20188, and later they further cyclized this large chromosome into a circular chromosome, like a typical prokaryotic chromosome9. This process greatly changed the 3D structure of the yeast genome. But surprisingly, the growth of this strain (with singular linear chromosome) is similar to that of the wild type8. Of course, its gene expression profile has changed significantly. Also in yeast, Jef Boeke team developed a method called SCRaMbLE, in which loxP sites are inserted into synthetic chromosomes and Cre recombinase is used to trigger chromosome rearrangements10-12. Many interesting results have been obtained using this method, which provides a great facility for the study of chromosome structure (including 3D structure) and function13. As multicellular organisms face many more challenges, such as cell differentiation, development and homeostasis, the mammalian genomes are more sophisticatedly regulated at both 3D structure and epigenetics level. Obviously, if similar studies can be performed in the mammalian cells, it would be more helpful for us to understand the roles of chromosome structure in the development and diseases. However, mammalian genomes are far larger and more complex than the yeast genome and a systematic method to induce chromosome rearrangements is yet absent, which limits the research in this field. In recent years, CRISPR-Cas9 genome editing technology has made great progress. Under the guidance of sgRNA, Cas9 endonuclease specifically cleaves DNA sequences, and the cleaved DNA strands were subsequently rejoined via non-homologous end joining (NHEJ) pathway14,15. There are large bioRxiv preprint doi: https://doi.org/10.1101/2021.06.15.448470; this version posted June 15, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. numbers of repetitive sequences in the mammalian genomes16. If sgRNAs are designed according these sequences, a large number of chromosome breaks can be generated, which will lead to systematic chromosome rearrangements (SCR) (Fig. 1A). Here, we developed a method called Chromosome Rearrangement by CRISPR-Cas9 (CReaC). We used sgRNAs to target endogenous retrotransposons, LINE-1 (L1) or Alu in HEK293T cells and obtained cells with significant different karyotypes from the control cells. Whole genome sequencing (WGS) showed that large numbers of inversions, translocations and CNVs have occurred. Then we further performed transcriptomic and epigenetic studies to evaluate the effect of the SCR on the cell physiological status. Results Experiment design and cell selection There are >500000 LINE-1 (intact elements and fragments) and >1000000 Alu copies in the human genome16, which provides an ideal set of targets for making multiple DNA DSBs using CRISPR-Cas9. We designed a sgRNA according to the ORF2 region of L1 and a sgRNA according to the most conservative region of Alu, which have 7398 and 317924 matching sites respectively in the current hg38 human genome haploid version (Fig. 1B). These sgRNAs were cloned into the pSB-CRISPR plasmid as previously described17 and a 20 nt sequences with no match in the human genome were used as negative control sgRNA. The plasmids (pSB-CRISPR-sgNC, pSB-CRISPR-sgL1 and pSB-CRISPR-sgAlu) were transfected together with the SB100X plasmids18 into HEK293T cells respectively. The cells were then kept in the presence of puromycin, forcing the Cas9 endonuclease and sgRNAs to express constantly and keep cleaving the chromosomes. The cells that survived after puromycin selection were designated as SCR-L1, SCR-Alu and NC respectively. As expected, the survival rates of SCR-L1 and SCR-Alu are lower than that of NC, due to the strong stress caused by multiple DSBs (Fig. 1C). The SCR-L1 and SCR-Alu cells recovered, and eventually grew up after roughly three weeks. Then, they started to proliferate stably, and there was no difference between the growth rates of the SCR and NC cells. Thus, new immortalized strains were created by targeting repetitive retroelements with CRISPR-Cas9 (Fig. 1D). To see if chromosome rearrangements really happened, cytogenetics assay was performed. SCR and NC cells were treated with the classical Giemsa Staining (Fig. 1E-H). It is known that HEK293 cells are female human cells with a karyotype near triploid19. Typical NC cells have 67 chromosomes as expected, while SCR cells bioRxiv